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TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.

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Τίτλος: TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.
Συγγραφείς: Wacker EM; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany., Rühlemann MC; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.; Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany., Franke A; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany., Ellinghaus D; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. d.ellinghaus@ikmb.uni-kiel.de.
Πηγή: Nature communications [Nat Commun] 2026 Jun 11; Vol. 17 (1). Date of Electronic Publication: 2026 Jun 11.
Τύπος έκδοσης: Journal Article; Research Support, Non-U.S. Gov't
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
Imprint Name(s): Original Publication: [London] : Nature Pub. Group
Ιατρικοί όροι (MeSH): Metagenome*/genetics , Metagenomics*/methods , Software*, Sequence Analysis, DNA/methods ; Humans ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Shotgun Sequencing ; Workflow
Περίληψη: Metagenomic shotgun sequencing data from over 600,000 metagenomes are publicly available in repositories such as NCBI's Sequence Read Archive (SRA). Technically advanced and easy-to-use best-practice metagenome software workflows for raw data pre-processing, assembly of metagenome-assembled genomes, and taxonomic and functional annotation of metagenome-assembled genomes are needed for reproducible analysis and harmonization of large-scale metagenomic datasets. We introduce TOFU-MAaPO (Taxonomic Or FUnctional Metagenomic Assembly and PrOfiling), a portable, automated single-command Nextflow pipeline for large-scale analysis of metagenomic short-read sequencing data. It analyzes metagenome files locally or directly from the SRA using accession or study IDs. In a benchmark against three established metagenome software pipelines, the TOFU-MAaPO workflow yielded 12%, 42% to 77% more high-quality metagenome-assembled genomes, likely reflecting the integration of multiple complementary binning tools with a unified refinement strategy. Using its assembly-free taxonomic abundance profiling module, we also automatically downloaded 16,462 uniquely identifiable and accessible human gut metagenome samples from the SRA and taxonomically annotated them against the Genome Taxonomy Database on a high-performance cluster in less than 55 hours, including download time. TOFU-MAaPO makes large metagenome projects more accessible to individual research groups and is freely available at https://github.com/ikmb/TOFU-MAaPO .
(© 2026. The Author(s).)
Competing Interests: Competing interests: The authors declare no competing interests.
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Grant Information: EL 831/5-1 Deutsche Forschungsgemeinschaft (German Research Foundation); EXC 2167/2 - 390884018 Deutsche Forschungsgemeinschaft (German Research Foundation)
Molecular Sequence: SRA SRP102150
Entry Date(s): Date Created: 20260611 Date Completed: 20260614 Latest Revision: 20260726
Update Code: 20260726
PubMed Central ID: PMC13260335
DOI: 10.1038/s41467-026-74033-9
PMID: 42277027
Βάση Δεδομένων: MEDLINE
Περιγραφή
ISSN:2041-1723
DOI:10.1038/s41467-026-74033-9